Patents by Inventor Mark Andersen

Mark Andersen has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).

  • Publication number: 20220065767
    Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.
    Type: Application
    Filed: November 12, 2021
    Publication date: March 3, 2022
    Inventors: Mark ANDERSEN, Michael PALLAS, Haopeng Wang
  • Patent number: 11193872
    Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.
    Type: Grant
    Filed: December 17, 2018
    Date of Patent: December 7, 2021
    Assignee: Life Technologies Corporation
    Inventors: Mark Andersen, Michael Pallas, Haopeng Wang
  • Patent number: 11130984
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.
    Type: Grant
    Filed: April 13, 2020
    Date of Patent: September 28, 2021
    Assignee: Life Technologies Corporation
    Inventors: Mark Andersen, Steven Roman
  • Patent number: 11118428
    Abstract: A method for performing a simulation of a field having a subterranean formation is described. The method includes obtaining phase behavior data of subterranean fluids of the field, generating an equation of state (EOS) model of the fluids based on the phase behavior data, generating a Helmholtz free energy model that reproduces predictions of the EOS model over a pre-determined pressure and temperature range, and performing the simulation of the field using the Helmholtz free energy model. The method may further include reducing the EOS model to a reduced EOS model having a reduced number of components to represent the EOS model over a pre-determined pressure and temperature range, generating the Helmholtz free energy model based on the reduced EOS model, and obtaining and using phase behavior data of injection fluids used. A computer system data.
    Type: Grant
    Filed: November 25, 2014
    Date of Patent: September 14, 2021
    Assignee: SCHLUMBERGER TECHNOLOGY CORPORATION
    Inventors: John Ratulowski, Denis Klemin, Mark Andersen, Oleg Dinariev, Nikolay Vyacheslavovich Evseev, Evgeny Ivanov, Sergey Sergeevich Safonov, Dmitry Anatolievich Koroteev
  • Patent number: 11001836
    Abstract: Provided are methods for preparing a library of target nucleic acid sequences, as well as compositions and uses therefor. Methods comprise contacting a nucleic acid sample with a plurality of adaptors capable of amplification of one or more target nucleic acid sequences under conditions wherein the target nucleic acid(s) undergo a first amplification; digesting the resulting first amplification products; repairing the digested target amplicons; and amplifying the repaired products in a second amplification, thereby producing a library of target nucleic acid sequence. Each of the plurality of adaptor compositions comprise a handle and a targeted nucleic acid sequence and optionally one or more tag sequences. Provided methods may be carried out in a single, addition only workflow reaction, allowing for rapid production of highly multiplexed targeted libraries, optionally including unique tag sequences. Resulting library compositions are useful for a variety of applications, including sequencing applications.
    Type: Grant
    Filed: June 29, 2018
    Date of Patent: May 11, 2021
    Assignee: Life Technologies Corporation
    Inventors: Mark Andersen, Daniel Mazur, Sihong Chen, Guobin Luo, Xinzhan Peng
  • Publication number: 20210032679
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
    Type: Application
    Filed: October 15, 2020
    Publication date: February 4, 2021
    Inventors: John LEAMON, Mark ANDERSEN, Michael THORNTON
  • Publication number: 20200399633
    Abstract: The present disclosure describes oligonucleotide-tethered nucleotides, methods of making them, and methods of using them. The oligonucleotide-tethered nucleotides comprise, in some embodiments, a nucleotide linked to an oligonucleotide of from about 3 to about 100 nucleotides in length. These oligonucleotide-tethered nucleotides can be used to label a plurality of different types of nucleic acids in a plurality of different situations with a known oligonucleotide, which can serve as a barcode in some embodiments. The resulting oligonucleotide-labeled nucleic acids oligonucleotides can be used in a variety of nucleic acid sequencing methods.
    Type: Application
    Filed: June 22, 2020
    Publication date: December 24, 2020
    Inventors: Arvydas LUBYS, Inga CIKOTIENE, Zana KAPUSTINA, Arturas BEREZNIAKOVAS, Justina MEDZIUNE, Simona ZEIMYTE, Mark ANDERSEN, Michael ALLEN, Sihong CHEN
  • Publication number: 20200377935
    Abstract: Provided are methods and compositions for reducing unfavorable dimer formation and thereby improving library preparation, e.g., for sequencing. Compositions and methods include adapters comprising extensive 5? overhang sequences and blunt end or T overhang 3? sequences to ends of target nucleic acid(s) to facilitate amplification and analysis of such sequences.
    Type: Application
    Filed: March 22, 2018
    Publication date: December 3, 2020
    Inventors: MARK ANDERSEN, MICHAEL ALLEN
  • Patent number: 10837052
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
    Type: Grant
    Filed: April 27, 2018
    Date of Patent: November 17, 2020
    Assignee: Life Technologies Corporation
    Inventors: John Leamon, Mark Andersen, Michael Thornton
  • Patent number: 10829811
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
    Type: Grant
    Filed: April 27, 2018
    Date of Patent: November 10, 2020
    Assignee: Life Technologies Corporation
    Inventors: John Leamon, Mark Andersen, Michael Thornton
  • Publication number: 20200340039
    Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
    Type: Application
    Filed: May 11, 2020
    Publication date: October 29, 2020
    Inventors: Mark ANDERSEN, David RUFF
  • Publication number: 20200239936
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.
    Type: Application
    Filed: April 13, 2020
    Publication date: July 30, 2020
    Inventors: Mark ANDERSEN, Steven ROMAN
  • Publication number: 20200224280
    Abstract: Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample.
    Type: Application
    Filed: January 13, 2020
    Publication date: July 16, 2020
    Inventors: Gordon A. JANAWAY, Mark ANDERSEN, Kornelija ZGONC, Michael C. PALLAS, Marcin SIKORA, Casey R. McFARLAND, Ferrier N. LE, Haopeng Wang, Jian GONG, Gothami Padmabandu
  • Patent number: 10689695
    Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
    Type: Grant
    Filed: October 17, 2017
    Date of Patent: June 23, 2020
    Assignee: Applied Biosystems, LLC
    Inventors: Mark Andersen, David Ruff
  • Patent number: 10620340
    Abstract: A method and computer system for performing simulation of a field having a subterranean formation. The method includes obtaining measured core sample data of a core sample retrieved from the formation, the core sample data measured by injecting fluid into the core sample, obtaining a digital rock model of the core sample describing a physical pore structure in the core sample, and obtaining a fluid model describing a physical property of the fluid. A digital core analysis (DCA) of the core sample is performed to generate a DCA simulation result and the DCA is tuned using the measured core sample data to reduce a difference between the DCA simulation result and the measured core sample data. The tuning is performed by adjusting, in response to the difference exceeding a pre-determined limit, a parameter of the DCA to generate an adjusted parameter and further performing the DCA to reduce the difference.
    Type: Grant
    Filed: October 2, 2014
    Date of Patent: April 14, 2020
    Assignee: SCHLUMBERGER TECHNOLOGY CORPORATION
    Inventors: Mark Andersen, Denis Klemin, Alexander Nikolaevich Nadeev
  • Patent number: 10619190
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for isolating nucleic acid molecules from a sample. In particular, the methods generally relate to normalizing the concentration of target nucleic acid molecules from a sample. In one aspect, the invention relates to purifying a primer extension product from a primer extension reaction mixture. In some aspects, nucleic acid molecules obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing.
    Type: Grant
    Filed: April 19, 2018
    Date of Patent: April 14, 2020
    Assignee: Life Technologies Corporation
    Inventors: Mark Andersen, Steven Roman
  • Patent number: 10557174
    Abstract: Methods and systems for quantification of a target nucleic acid in a sample are provided. The method includes forming a plurality of discrete sample portions. Each of the plurality of discrete sample portions comprising a portion of the sample, and a reaction mixture. The method further includes amplifying the plurality of discrete sample portions to form a plurality of discrete processed sample portions. At least one discrete processed sample portion containing nucleic acid amplification reaction products. Fluorescence signals are detected from the at least one of the plurality of discrete processed sample portions to determine a presence of the at least one target nucleic acid. The method also includes determining the respective volumes of the plurality of the plurality of discrete processed sample portions, and estimating the number of copies-per-unit-volume of the at least one target nucleic acid in the sample.
    Type: Grant
    Filed: March 25, 2016
    Date of Patent: February 11, 2020
    Assignee: Life Technologies Corporation
    Inventors: Gordon A. Janaway, Mark Andersen, Kornelija Zgonc, Michael C. Pallas, Marcin Sikora, Casey R. McFarland, Ferrier N. Le, Haopeng Wang, Jian Gong, Gothami Padmabandu
  • Patent number: 10465483
    Abstract: A method for performing simulation of a field having a subterranean formation, including: obtaining a three-dimensional (3D) porous solid image of a core sample, the core sample representing a portion of the field; generating a digital rock model from the solid image, the digital rock model describing a physical pore structure in the core sample; obtaining phase behavior data of fluids of the field; generating a digital fluid model of the fluids based on the phase behavior data, the digital fluid model describing a physical property of the fluid; performing, on a computer system and based on the digital rock model and the digital fluid model, simulations of the field by varying an input parameter for the simulations; and analyzing an output parameter generated by the simulations to determine an effect of varying the input parameter on the output parameter.
    Type: Grant
    Filed: July 23, 2014
    Date of Patent: November 5, 2019
    Assignee: SCHLUMBERGER TECHNOLOGY CORPORATION
    Inventors: Mark Andersen, Denis Klemin, Alexander Nikolaevich Nadeev, Omer M. Gurpinar, John Ratulowski
  • Patent number: 10266881
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
    Type: Grant
    Filed: July 10, 2015
    Date of Patent: April 23, 2019
    Assignee: Life Technologies Corporation
    Inventors: John Leamon, Mark Andersen, Michael Thornton
  • Publication number: 20190113430
    Abstract: A method of aligning a plurality of targets is provided. The method includes generating a plurality of targets. A third phase includes the plurality of targets. The method further includes combining a first phase, a second phase, and the third phase in a volume. The first phase, the second phase, and the third phase are substantially immiscible, and the third phase is in fluid communication with the first phase and the second phase, and the first phase, the second phase, and the third phase are operable to be in a configuration of the third phase between the first phase and the second phase in the volume.
    Type: Application
    Filed: December 17, 2018
    Publication date: April 18, 2019
    Inventors: Mark ANDERSEN, Michael PALLAS, Haopeng Wang